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Rajendrakumar AL, Hapca SM, Nair ATN, Huang Y, Chourasia MK, Kwan RSY, Nangia C, Siddiqui MK, Vijayaraghavan P, Matthew SZ, Leese GP, Mohan V, Pearson ER, Doney ASF, Palmer CNA. Competing risks analysis for neutrophil to lymphocyte ratio as a predictor of diabetic retinopathy incidence in the Scottish population. BMC Med 2023; 21:304. [PMID: 37563596 PMCID: PMC10413718 DOI: 10.1186/s12916-023-02976-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Diabetic retinopathy (DR) is a major sight-threatening microvascular complication in individuals with diabetes. Systemic inflammation combined with oxidative stress is thought to capture most of the complexities involved in the pathology of diabetic retinopathy. A high level of neutrophil-lymphocyte ratio (NLR) is an indicator of abnormal immune system activity. Current estimates of the association of NLR with diabetes and its complications are almost entirely derived from cross-sectional studies, suggesting that the nature of the reported association may be more diagnostic than prognostic. Therefore, in the present study, we examined the utility of NLR as a biomarker to predict the incidence of DR in the Scottish population. METHODS The incidence of DR was defined as the time to the first diagnosis of R1 or above grade in the Scottish retinopathy grading scheme from type 2 diabetes diagnosis. The effect of NLR and its interactions were explored using a competing risks survival model adjusting for other risk factors and accounting for deaths. The Fine and Gray subdistribution hazard model (FGR) was used to predict the effect of NLR on the incidence of DR. RESULTS We analysed data from 23,531 individuals with complete covariate information. At 10 years, 8416 (35.8%) had developed DR and 2989 (12.7%) were lost to competing events (death) without developing DR and 12,126 individuals did not have DR. The median (interquartile range) level of NLR was 2.04 (1.5 to 2.7). The optimal NLR cut-off value to predict retinopathy incidence was 3.04. After accounting for competing risks at 10 years, the cumulative incidence of DR and deaths without DR were 50.7% and 21.9%, respectively. NLR was associated with incident DR in both Cause-specific hazard (CSH = 1.63; 95% CI: 1.28-2.07) and FGR models the subdistribution hazard (sHR = 2.24; 95% CI: 1.70-2.94). Both age and HbA1c were found to modulate the association between NLR and the risk of DR. CONCLUSIONS The current study suggests that NLR has a promising potential to predict DR incidence in the Scottish population, especially in individuals less than 65 years and in those with well-controlled glycaemic status.
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Affiliation(s)
- Aravind Lathika Rajendrakumar
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
- Biodemography of Aging Research Unit, Duke University, Durham, NC, 27708-0408, USA
| | - Simona M Hapca
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
- Division of Computing Science and Mathematics, University of Stirling, Stirling, FK9 4LA, Scotland
| | | | - Yu Huang
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
| | - Mehul Kumar Chourasia
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
- IQVIA, 3 Forbury Place, 23 Forbury Road, Reading, RG1 3JH, UK
| | - Ryan Shun-Yuen Kwan
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
- Beatson Institute for Cancer Research, Glasgow, UK
| | - Charvi Nangia
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
| | - Moneeza K Siddiqui
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
- Wolfson Institute of Population Health, Queen Mary University of London, London, E1 4NS, UK
| | | | | | - Graham P Leese
- Department of Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | | | - Ewan R Pearson
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
| | - Alexander S F Doney
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK
| | - Colin N A Palmer
- Division of Population Health and Genomics, Ninewells Hospital, University of Dundee, Dundee, UK.
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Ruan D, Yang J, Zhuang Z, Ding R, Huang J, Quan J, Gu T, Hong L, Zheng E, Li Z, Cai G, Wang X, Wu Z. Assessment of Heterozygosity and Genome-Wide Analysis of Heterozygosity Regions in Two Duroc Pig Populations. Front Genet 2022; 12:812456. [PMID: 35154256 PMCID: PMC8830653 DOI: 10.3389/fgene.2021.812456] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/15/2021] [Indexed: 01/02/2023] Open
Abstract
Heterozygosity can effectively reflect the diverse models of population structure and demographic history. However, the genomic distribution of heterozygotes and the correlation between regions of heterozygosity (runs of heterozygosity, ROHet) and phenotypes are largely understudied in livestock. The objective of this study was to identify ROHet in the Duroc pig genome, and investigate the relationships between ROHet and eight important economic traits. Here, we genotyped 3,770 American Duroc (S21) and 2,096 Canadian Duroc (S22) pigs using 50 K single nucleotide polymorphism array to analyze heterozygosity. A total of 145,010 and 84,396 ROHets were characterized for S21 and S22 populations, respectively. ROHet segments were mostly enriched in 1–2 Mb length classification (75.48% in S21 and 72.25% in S22). The average genome length covered by ROHet was 66.53 ± 12.20 Mb in S21 and 73.32 ± 13.77 Mb in S22 pigs. Additionally, we detected 20 and 13 ROHet islands in S21 and S22 pigs. Genes in these genomic regions were mainly involved in the biological processes of immunity and reproduction. Finally, the genome-wide ROHet-phenotypes association analysis revealed that 130 ROHets of S21 and 84 ROHets of S22 were significantly associated with eight economic traits. Among the candidate genes in the significant ROHet regions, 16 genes related to growth, metabolism, and meat quality were considered as candidate genes for important economic traits of pigs. This work preliminarily explores the effect of heterozygosity-rich regions in the pig genome on production performance and provides new insights for subsequent research on pig genetic improvement.
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Affiliation(s)
- Donglin Ruan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
| | - Jinyan Huang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Ting Gu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Linjun Hong
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Zicong Li
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
| | - Gengyuan Cai
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
| | - Xiaopeng Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- *Correspondence: Xiaopeng Wang, ; Zhenfang Wu,
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, Guangzhou, China
- Guangdong Wens Breeding Swine Technology Co., Ltd., Yunfu, China
- *Correspondence: Xiaopeng Wang, ; Zhenfang Wu,
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Park B, An J, Kim W, Kang HY, Koh SB, Oh B, Jung KJ, Jee SH, Kim WJ, Cho MH, Silverman EK, Park T, Won S. Effect of 6p21 region on lung function is modified by smoking: a genome-wide interaction study. Sci Rep 2020; 10:13075. [PMID: 32753590 PMCID: PMC7403370 DOI: 10.1038/s41598-020-70092-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
Smoking is a major risk factor for chronic obstructive pulmonary disease (COPD); however, more than 25% of COPD patients are non-smokers, and gene-by-smoking interactions are expected to affect COPD onset. We aimed to identify the common genetic variants interacting with pack-years of smoking on FEV1/FVC ratios in individuals with normal lung function. A genome-wide interaction study (GWIS) on FEV1/FVC was performed for individuals with FEV1/FVC ratio ≥ 70 in the Korea Associated Resource cohort data, and significant SNPs were validated using data from two other Korean cohorts. The GWIS revealed that rs10947231 and rs8192575 met genome-wide significant levels; For \documentclass[12pt]{minimal}
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\begin{document}$${\text{H}}_{0} :\beta_{SNP} = \beta_{SNP*pack - years} = 0{\text{ vs H}}_{1} : not {\text{H}}_{0} ,$$\end{document}H0:βSNP=βSNP∗pack-years=0vs H1:notH0, the likelihood ratio (LR) test was conducted, and its P values, PLR, for rs10947231 and rs8192575 were 2.23 × 10–12 and 1.18 × 10–8, respectively. Interaction between rs8192575 and smoking is significantly replicated with two additional data (PINT = 0.0454, 0.0131). Expression quantitative trait loci, topologically associated domains, and PrediXcan analyses revealed that rs8192575 is significantly associated with AGER expression. SNPs on the 6p21 region are associated with FEV1/FVC, and the effect of smoking on FEV1/FVC differs among the associated genotypes.
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Affiliation(s)
- Boram Park
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Jaehoon An
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Wonji Kim
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Hae Yeon Kang
- Department of Internal Medicine, Healthcare Research Institute, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, South Korea
| | - Sang Baek Koh
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, Wonju, South Korea
| | - Bermseok Oh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun Ha Jee
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon University, Chuncheon, South Korea
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Taesung Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea. .,Department of Statistics, Seoul National University, Seoul, South Korea.
| | - Sungho Won
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea. .,Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea. .,Institute of Health and Environment, Seoul National University, Seoul, South Korea.
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